If for example I have a wx scope gui and an fft gui stacked one above
the other so I can see them simultaneously, the lower plot is missing
half of the lower portion off the bottom of the screen, i.e it doesnt
scale itself to fit within the confines of the visible screen.

It may not do it dynamically, but did you know you can enter dimensions
in the Window Size field for the scope and waterfall sink? I assume your
screen doesn't change size too often, so it should at least get it to a
point where it's usable for you.